Contacts of the helix formed by residues 161 - 177 (chain D) in PDB entry 4OGB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 161 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TYR* 3.6 17.6 - - - -
154D HIS 3.7 14.1 - - - +
157D VAL 2.9 26.9 + - - +
158D ALA 3.2 20.0 + - - -
159D TYR 2.6 11.8 + - - +
160D HIS* 1.3 74.3 - - - +
162D ASN* 1.3 69.2 + - - +
163D ILE* 2.9 22.1 + - - +
164D HIS* 3.2 9.7 + - - +
165D ALA 3.1 17.7 + - - -
332D TRP* 5.1 0.9 - - - -
335D ARG* 3.6 13.5 - - - +
510D EDO 3.6 14.1 + - - -
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Residues in contact with ASN 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ASN* 2.9 31.1 + - - -
117D PRO* 3.5 5.5 - - - +
118D LEU* 4.0 4.2 - - + +
150D GLU* 2.9 34.4 + - + +
153D TYR* 3.5 18.0 - - + +
161D ASN* 1.3 73.0 - - - +
163D ILE* 1.3 60.3 + - - -
165D ALA* 3.3 5.1 + - - +
166D ALA* 2.9 28.2 + - - +
508D DMS 3.3 22.9 - - + +
510D EDO 2.9 26.9 + - - -
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Residues in contact with ILE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 4.1 23.7 - - + +
107D PHE* 3.9 19.5 - - + -
110D ALA* 4.0 24.5 - - + -
115D ASN* 4.5 0.4 - - - +
117D PRO* 4.0 9.6 - - + -
161D ASN* 2.9 8.6 + - - +
162D ASN* 1.3 82.6 - - - +
164D HIS* 1.3 61.9 + - - +
166D ALA* 3.3 2.5 + - - +
167D ASP* 2.9 27.9 + - - +
332D TRP* 3.8 17.7 - - + -
335D ARG* 4.1 21.8 - - - +
510D EDO 3.4 23.6 - - - +
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Residues in contact with HIS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D TYR* 3.1 57.8 + + - +
160D HIS* 4.2 9.4 - + - -
161D ASN* 3.2 7.0 + - - +
163D ILE* 1.3 76.7 - - - +
165D ALA* 1.3 65.6 + - - +
167D ASP* 3.2 6.7 + - - +
168D VAL* 2.9 37.4 + - + +
200D HIS* 3.3 7.4 + + - -
201D ASP* 3.0 21.1 + - + -
318D ASP* 3.1 13.7 + - - -
321D ASN* 5.1 1.9 + - - -
332D TRP* 3.8 15.7 - - + -
512D ZN 2.2 29.8 - - - -
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Residues in contact with ALA 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 4.0 9.2 - - + -
153D TYR* 3.4 44.6 - - + +
161D ASN 3.1 6.0 + - - +
162D ASN 3.6 8.3 - - - +
164D HIS* 1.3 78.0 - - - +
166D ALA* 1.3 57.7 + - - +
168D VAL* 3.2 2.8 + - - +
169D VAL* 2.9 33.6 + - - +
197D SER 4.2 1.6 - - - +
198D ALA 3.9 7.9 - - - +
200D HIS* 4.6 12.1 - - - -
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 4.2 1.6 - - + -
117D PRO* 3.7 18.4 - - + +
118D LEU* 3.7 34.2 - - - +
121D ILE* 3.9 15.3 - - + +
162D ASN 2.9 17.4 + - - +
163D ILE 3.6 4.9 - - - +
165D ALA* 1.3 76.8 - - - +
167D ASP* 1.3 56.6 + - - +
169D VAL* 3.4 4.5 + - - +
170D GLN* 3.0 30.0 + - - +
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Residues in contact with ASP 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 4.3 16.5 - - + +
163D ILE 2.9 17.7 + - - +
164D HIS* 3.2 8.3 + - - +
166D ALA* 1.3 76.8 - - - +
168D VAL* 1.3 60.1 + - - +
170D GLN* 3.3 7.2 + - - +
171D SER* 2.8 34.1 + - - -
317D ALA 5.2 0.2 - - - +
320D SER* 4.2 3.8 + - - -
321D ASN* 3.4 24.8 + - - -
324D LYS* 3.0 28.1 + - - -
332D TRP* 3.6 24.7 + - + -
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Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D HIS* 2.9 45.1 + - + +
165D ALA 3.8 1.8 - - - +
167D ASP* 1.3 75.7 - - - +
169D VAL* 1.3 62.0 + - - +
171D SER* 4.3 4.9 - - - -
172D THR* 2.9 34.5 + - - +
197D SER* 3.8 18.8 - - - +
200D HIS* 3.6 24.5 - - + +
314D VAL* 4.5 7.0 - - + +
317D ALA* 3.8 19.4 - - + +
318D ASP* 3.9 18.2 - - + +
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU* 4.0 5.4 - - + -
121D ILE* 4.5 3.6 - - + -
122D MET* 3.5 26.5 - - + -
125D ILE* 3.8 19.3 - - + -
165D ALA 2.9 18.8 + - - +
166D ALA* 3.5 9.4 - - - +
168D VAL* 1.3 77.1 - - - +
170D GLN* 1.3 58.7 + - - +
172D THR* 3.3 2.8 + - - -
173D HIS* 2.9 26.5 + - - +
194D ILE* 4.1 11.8 - - + +
197D SER* 3.7 8.1 - - - -
198D ALA* 3.4 42.0 - - + +
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Residues in contact with GLN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 2.9 37.8 + - + +
101D LYS 2.7 28.2 + - - +
102D TRP* 4.8 1.6 - - - +
103D GLY 5.0 0.9 + - - -
104D LEU* 3.6 37.0 + - + +
121D ILE* 4.0 9.6 - - + -
125D ILE* 4.0 8.7 - - - -
166D ALA 3.0 16.8 + - - +
167D ASP* 3.3 7.6 + - - +
169D VAL* 1.3 76.2 - - - +
171D SER* 1.3 69.8 + - - +
173D HIS* 3.2 3.8 + - - +
174D VAL* 3.0 34.3 + - - +
324D LYS* 4.6 6.6 + - - -
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Residues in contact with SER 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D TRP* 3.7 22.8 - - - -
167D ASP* 2.8 21.4 + - - -
168D VAL* 4.3 0.7 - - - -
170D GLN* 1.3 77.9 + - - +
172D THR* 1.3 65.1 + - - +
174D VAL* 3.2 1.4 + - - -
175D LEU* 2.9 26.7 + - - +
317D ALA* 3.7 21.1 - - - -
320D SER* 3.6 7.3 + - - -
324D LYS* 2.8 28.2 + - - -
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Residues in contact with THR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL 2.9 15.5 + - - -
169D VAL 3.6 3.4 - - - -
171D SER* 1.3 76.3 - - - +
173D HIS* 1.3 56.9 + - - +
175D LEU* 3.1 6.8 + - - +
176D LEU* 2.8 48.2 + - + +
193D ALA* 4.0 19.3 - - + +
194D ILE* 4.7 3.4 - - + +
197D SER* 2.8 28.8 + - - +
313D MET* 4.2 8.3 - - + -
314D VAL* 3.9 12.6 - - + +
317D ALA* 3.4 15.7 - - - +
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Residues in contact with HIS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 3.4 25.6 - - - +
100D ASN* 2.7 25.7 + - - -
125D ILE* 3.7 34.9 - - + +
128D GLU* 4.6 5.3 - - + +
129D ARG* 2.9 53.8 + - + +
169D VAL 2.9 13.8 + - - +
170D GLN 3.3 7.6 - - - +
172D THR* 1.3 76.8 - - - +
174D VAL* 1.3 61.2 + - + +
176D LEU* 4.5 5.8 - - - -
177D SER* 2.8 26.0 + - - -
194D ILE* 5.1 3.8 - - + +
511D EDO 3.7 19.2 + - - -
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Residues in contact with VAL 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL 4.1 2.7 - - - +
100D ASN* 3.6 22.7 - - - +
101D LYS 4.1 4.5 - - - +
102D TRP* 3.7 24.9 - - + +
170D GLN* 3.0 36.7 + - - +
171D SER 3.2 6.5 + - - +
173D HIS* 1.3 75.5 - - - +
175D LEU* 1.3 64.9 + - - +
177D SER* 3.0 18.2 + - - -
178D THR 3.4 7.4 + - - -
503D EDO 4.2 10.7 - - - +
516D PEG 3.7 26.7 - - - +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TRP* 3.8 13.7 - - + -
171D SER 2.9 20.9 + - - +
172D THR 3.7 1.6 - - - +
174D VAL* 1.3 75.9 - - - +
176D LEU* 1.3 61.8 + - - +
178D THR* 3.2 24.8 + - - +
181D LEU* 3.9 5.9 - - - +
313D MET* 3.5 46.7 - - + +
316D CYS* 3.9 6.3 - - + -
317D ALA* 4.0 9.9 - - + +
381D TRP* 3.8 36.3 - - + -
384D TRP* 4.1 9.8 - - + +
395D ILE* 4.6 0.2 - - + -
503D EDO 3.8 26.2 + - - +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ARG* 3.5 18.7 + - - +
172D THR* 2.8 33.0 + - + +
173D HIS* 4.5 0.2 - - - -
174D VAL 3.2 0.2 - - - -
175D LEU* 1.3 77.3 - - - +
177D SER* 1.3 58.4 + - - +
178D THR 3.3 2.2 + - - +
181D LEU* 4.3 17.7 - - - +
182D GLU* 5.7 0.3 - - - -
185D PHE* 4.2 19.8 - - + -
190D ILE* 4.1 35.2 - - + +
193D ALA* 4.3 3.1 - - + -
194D ILE* 3.9 23.3 - - + -
310D LEU* 4.5 7.6 - - + -
313D MET* 3.6 28.5 - - + -
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Residues in contact with SER 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ASN* 6.0 2.0 - - - +
129D ARG* 3.0 13.2 + - - +
173D HIS* 2.8 22.3 + - - -
174D VAL* 3.0 12.2 + - - -
176D LEU* 1.3 75.8 - - - +
178D THR* 1.3 65.1 + - - +
182D GLU* 6.2 0.7 - - - -
504D DMS 3.1 31.8 - - - +
511D EDO 3.2 18.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il